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House leaders proposed a $33.8 billion budget Wednesday for the upcoming fiscal year that would boost funding for higher education and local aid but would reject Governor Deval Patrick’s push for universal prekindergarten, one of his top priorities.

The plan represents a second setback for the governor, after House lawmakers earlier this week scuttled his $1.9 billion tax hike for education and transportation in favor of a $500 million tax increase focused more narrowly on shoring up the MBTA and regional transit authorities.

Overall, the House budget unveiled Wednesday would chop $1 billion out of the $34.8 billion budget that Patrick proposed in January and would increase spending by 3.9 percent, compared to the 6.9 percent increase Patrick wants. Patrick and the Legislature must resolve their differences and approve a budget by ­July 1, when the new fiscal year begins.

While the governor proposed using his $1.9 billion tax hike to build rail lines across the state and eliminate the waiting list for prekindergarten programs, most of the spending increases in the House plan would be limited to essentials such as state debt payments, pension obligations, collective bargaining agreements, and entitlement programs like Medicare. There are even a few cuts, including a reduc­tion in funding for youth jobs and civil legal aid for the poor.

“While very pleased to see that the House has shown their strong support for higher education, I am concerned about this budget’s failure to invest in a number of vital programs like youth violence prevention and early education that the governor believes are critical to the future of our state,” said Glen Shor, Patrick’s budget chief.

Liberal groups were also disappointed. “It’s a missed opportunity,” said Noah Berger, president of the Massachusetts Budget and Policy Center, a left-leaning think tank. “The governor had proposed a forward-­looking effort to invest significantly in education. ­Obviously, that took revenue to pay for. In not doing that new revenue, it became impossible to make those investments.”

The House budget chief, Representative Brian Dempsey of Haverhill, said House leaders were concerned that the governor’s budget went too far in pushing higher taxes and spending, since “families across the Commonwealth continue to struggle in this economy.”

“We needed to deal with ­issues like transportation, but do it in a way that was well ­balanced and mindful of the current economic climate that we’re in,” he said.

While the fight between ­Patrick and legislative leaders over taxes and transportation funding has drawn most of the attention on Beacon Hill, the House budget made clear the extent to which the governor and the House are sharply at odds over prekindergarten programs, as well.

Patrick has been pushing for an additional $131 million for subsidized day care for children from birth to age 5, arguing those programs build the foundation for learning later in life.

Patrick’s budget would have eliminated the list of 30,000 children waiting for programs and funded higher salaries, professional development, and grants for programs that want to expand.

But Speaker Robert A. ­DeLeo said the House budget would not provide any increase for early education, because he is concerned that the state agency that oversees the system is not managing its money and caseload efficiently.

DeLeo questioned how the Department of Early Education and Care’s waiting list had jumped from 30,000 to 50,000 over the last few months and why, if there is a waiting list for services, the agency has ended the last two years with a surplus. Sherri Killins, the agency’s commissioner, also resigned last month amid criticism that she was neglecting her official duties to take part in a superintendent training program in Central Massachusetts.

DeLeo said his budget would order state Auditor ­Suzanne Bump to review the department’s finances and waiting list and create a $200,000 “compliance office” to scrutinize the thousands of child-care providers that the ­department licenses.

“Before we make any further investments, we want to make sure their house is in order,” ­DeLeo said.

Thomas L. Weber, acting Commissioner of the Department of Early Education and Care, said DeLeo is conflating two waiting lists — one for pre-K programs that has 30,000 children and one for after-school programs that has 20,000. Weber also said the agency has had small surpluses because it wants to avoid running a deficit at the end of the year, which could force it to ­remove children from day-care programs.

Weber said the House budget, by not providing any additional money for early education, would increase the waiting list for pre-K programs to 42,000 children by July 2014.

The House budget also seeks to crack down on welfare fraud following a recent report by the inspector general, who found that the Patrick administration has been handing out $25 million in welfare benefits annually to recipients who cannot prove they are eligible.

The House plan responds by creating a $300,000 Bureau of Program Integrity to root out welfare fraud. The budget also would require photos on ­Electronic Benefit Transfer cards, to prevent trafficking of the cards. That idea has been pushed by Republicans in the Legislature.

Higher education is one area where DeLeo and Patrick agree.

The House budget, like the governor’s budget, seeks an ­increase of $110 million for higher education, including an additional $39 million for the University of Massachusetts and $30 million for community colleges. If approved, the ­increases would allow the ­UMass system to freeze tuitions and fees at their current level, DeLeo said.

“We’re pleased with it,” said Martin T. Meehan, chancellor of UMass Lowell. “It’s a modest increase that would only bring us to where we were under Mitt Romney but, nonetheless, it’s welcome news and a reversal of a trend” of cuts over the last five years.

Local aid would see an ­increase of $21 million in the House budget, less than the $31 million Patrick proposed. But Geoff Beckwith, executive ­director of the Masssachusetts Municipal Association, praised the budget because it would give the money to cities and towns without strings.